© 2016 Elsevier Ltd In this study, a numerical manifold method (NMM) model is developed to analyze flow in porous media with discrete fractures in a non-conforming mesh. This new model is based on a two-cover-mesh system with a uniform triangular mathematical mesh and boundary/fracture-divided physical covers, where local independent cover functions are defined. The overlapping parts of the physical covers are elements where the global approximation is defined by the weighted average of the physical cover functions. The mesh is generated by a tree-cutting algorithm. A new model that does not introduce additional degrees of freedom (DOF) for fractures was developed for fluid flow in fractures. The fracture surfaces that belong to different physical covers are used to represent fracture flow in the direction of the fractures. In the direction normal to the fractures, the fracture surfaces are regarded as Dirichlet boundaries to exchange fluxes with the rock matrix. Furthermore, fractures that intersect with Dirichlet or Neumann boundaries are considered. Simulation examples are designed to verify the efficiency of the tree-cutting algorithm, the calculation's independency from the mesh orientation, and accuracy when modeling porous media that contain fractures with multiple intersections and different orientations. The simulation results show good agreement with available analytical solutions. Finally, the model is applied to cases that involve nine intersecting fractures and a complex network of 100 fractures, both of which achieve reasonable results. The new model is very practical for modeling flow in fractured porous media, even for a geometrically complex fracture network with large hydraulic conductivity contrasts between fractures and the matrix.